Bioinformatics Databases Research Articles

Elsholtzia bodinieri Vaniot Ameliorated Acute Lung Injury by NQO1, BCL2 and PTGS2 In Silico and In Vitro Analyses

Acute lung injury (ALI) is a clinical respiratory disease caused by various factors, which lacks effective pharmacotherapy to reduce the mortality rate. Elsholtzia bodinieri Vaniot is an annual herbaceous plant used as a traditional herbal tea and folk medicine. Here we used bioinformatic databases and software to explore and analyze the potential key genes in ALI regulated by E. bodinieri Vaniot, including B cell leukemia/lymphoma 2 (Bcl2), prostaglandin-endoperoxide synthase 2 (Ptgs2) and NAD(P)H dehydrogenase, quinone 1 (Nqo1). In an inflammatory cells model, we verified bioinformatics results, and further mechanistic analysis showed that methanol extract of E. bodinieri Vaniot (EBE) could alleviate oxidative stress by upregulating the expression of NQO1, suppress pyroptosis by upregulating the expression of BCL2, and attenuate inflammation by downregulating the expression of PTGS2. In sum, our results demonstrated that EBE treatment could alleviate oxidative stress, suppress pyroptosis and attenuate inflammation by regulating NQO1, BCL2 and PTGS2 in a cells model, and E. bodinieri Vaniot might be a promising source for functional food or as a therapeutic agent.

Experiences from 4 Years of Organization of an External Quality Assessment for Mycobacterium tuberculosis Whole-Genome Sequencing in the European Union/European Economic Area.

Here, we report the development and key features of the first external quality assessment (EQA) scheme for Mycobacterium tuberculosis whole-genome sequencing (WGS). The results of four rounds (2017 to 2020) of implementation within the European tuberculosis reference laboratories network (ERLTB-Net-2) are presented and discussed. EQA panels comprising 10 genomic DNAs were distributed to ERLTB-Net 2 laboratories volunteering to participate in this exercise. Since 2018, five FASTQ files were added to better assess the dry WGS processes, and in 2020, three of the five files were replaced by synthetic files (providing additional flexibility for the mutations included in the panels). Ten National tuberculosis reference laboratories participated in all four EQA rounds, and seven participated in at least one. High-confidence resistance mutations were correctly identified by all laboratories, but challenges remained with respect to the identification of mixed loci and interpretation of rare mutations. M. tuberculosis genotyping and clustering analysis was >90% accurate for pure samples with the main challenges being related to the analysis of mixed genotypes and DNA FASTQ files. The development and implementation of this WGS EQA scheme has contributed to the continuous improvement in performance of participating laboratories in M. tuberculosis WGS and data analysis. This scheme can serve as a model of comprehensive quality assessment for M. tuberculosis WGS that can be replicated in different settings worldwide. IMPORTANCE The wider availability of whole-genome sequencing (WGS) coupled to new developments in bioinformatic tools and databases to interpret Mycobacterium tuberculosis complex WGS data has accelerated the adoption of this method for the routine prediction of antimycobacterial drug resistance and genotyping, thus necessitating the establishment of a comprehensive external quality control system. Here, we report 4 years of development and results from such a panel.

FineFDR: Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics.

Microbial community proteomics, also termed metaproteomics, investigates all proteins expressed by a microbiota. Tandem mass spectrometry (MS/MS) is the typical method for identifying proteins in metaproteomics, which involves searching the mass spectra against a protein sequence database. A major post-analysis step is controlling the false discovery rate (FDR), i.e., the ratio of false positives to the total number of annotations. The current popular target-decoy FDR estimation method treats all the peptides and proteins equally and overlooks that they could have varied probabilities of being identified. In this study, we report FineFDR, a framework for FDR assessment at fine-grained levels with taxonomy information considered. FineFDR groups the identified peptide-spectrum matches, peptides, and proteins from different taxonomic units and estimates the FDR in each group separately. Empirical experiments on the simulated and real-world data sets demonstrate that our FineFDR achieved higher precision and more peptide and protein identifications when compared to the state-of-the-art methods, such as Comet, Percolator, TIDD, and Tailor. FineFDR is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/FDR.

MiRNAs secreted by human blastocysts could be potential gene expression regulators during implantation.

Micro RNAs (miRNAs) are small non-coding RNAs known as essential regulators of cell-cell communication. Recent studies have revealed that miRNAs are secreted by a blastocyst in culture media. We hypothesized that endometrial epithelial cells take up embryo-derived miRNAs as well as other soluble factors and regulate their receptivity-related gene expression. Blastocyst culture media (BCM) were collected from the individually cultured embryos, while human endometrial epithelial cells (HEECs) were collected from healthy fertile volunteers. To evaluate the effect of BCM on the endometrial receptivity gene expression, HEECs were co-cultured with implanted BCM, non-implanted BCM, and a control culture medium. After determining altered gene expression in the HEECs, the miRNAs-related genes through bioinformatics databases were identified and evaluated in the BCM. Co-culture of primary HEECs with BCM significantly stimulated the expression levels of VEGFA, HBEGF, HOXA10, and LIF in the implanted group compared with non-implanted and control groups. The fold changes of miR-195 significantly diminished in the implanted BCM group compared with the non-implanted BCM group. Reduced fold changes of miR-29b, 145 and increased miR-223 were also observed in the implanted BCM group compared with the non-implanted ones. miRNAs could function as potential gene expression regulators during implantation. These molecules are secreted by human blastocyst, taken up by endometrial epithelial cells, and cause a change in the endometrial function. We found that BCMs can be effective in implantation process by stimulating related receptivity gene expression.

GSPT1 Functions as a Tumor Promoter in Human Liver Cancer.

This study analyzed the role of G1 to S phase transition 1 protein (GSPT1) in promoting progression of liver cancer cells. A bioinformatics database was used to analyze the expression levels of GSPT1 in liver cancer tissues and the prognosis of patients. Subsequently, Western blotting and quantitative PCR were used to verify the expression levels of GSPT1 between normal hepatocytes and hepatoma cells. We used a CRISPR/Cas9 system to construct knockouts of GSPT1 in HepG2 and HCCLM9 liver cancer cells. The effect of GSPT1 on liver cancer cell migration and invasion was analyzed using flow cytometry, migration, and tumor formation assays. The Cancer Genome Atlas Liver Hepatocellular Carcinoma dataset indicated that GSPT1 expression was upregulated in liver cancer cell lines, and patients with liver cancer had poor prognosis. Knockout of GSPT1 in cells significantly inhibited tumor proliferation, cell migration, and growth in vivo. In this study, we found that GSPT1 promotes the migration and invasion of liver cancer cells.

Genetic variant in miR-17-92 cluster binding sites is associated with esophageal squamous cell carcinoma risk in Chinese population

BackgroundSingle nucleotide polymorphisms (SNPs) located in microRNA (miRNA) binding sites can affect the interactions between miRNAs and target genes, which is related to cancer susceptibility and tumorigenesis. However, the association between SNPs located in miR-17-92 cluster binding sites and ESCC risk remains unclear. Therefore, we aimed to explore the relationship between polymorphisms in miR-17-92 cluster binding sites and ESCC susceptibility.MethodsSix SNPs in the binding sites of miR-17-92 cluster were selected using bioinformatics databases, and their association with ESCC risk was investigated in a case-control study (including 488 cases and 512 controls) based on the population from high incidence areas of ESCC in China. We evaluated the SNP-SNP and SNP-smoking interactions using generalized multifactor dimensionality reduction (GMDR). Moreover, the expression of the miR-17-92 cluster and its target genes was determined in ESCC and adjacent normal tissues by quantitative real-time polymerase chain reaction (qRT-PCR). The dual-luciferase reporter assay was conducted to verify the effect of SNPs on the binding affinity between miRNAs and target genes.ResultsWe found that the SNP rs1804506 C > T had a significant association with the decreased ESCC risk. The SNP rs1804506 T allele was associated with a significantly decreased risk of ESCC in the additive model (OR = 0.817, 95% CI = 0.681–0.981, P = 0.030). The rs1804506 T allele had more striking effects on reducing ESCC risk in older individuals, female or non-smoker subgroups. We also found a significant interaction effect between rs1366600 and smoking by GMDR methods (P = 0.011). Additionally, the expression levels of miR-19a-3p and TGFBR3 were significantly downregulated in ESCC tissues compared with normal tissues, and the carriers of rs1804506 TT genotype had lower expression level of TGFBR3 than those of rs1804506 CC/CT genotype. Following dual-luciferase reporter assay showed that the rs1804506 T allele reduced the binding of miR-19a-3p and TGFBR3 3′-UTR.ConclusionsOur findings suggest that the rs1804506 polymorphism in miR-17-92 cluster binding sites contributes to the susceptibility of ESCC, which might provide new clues and scientific evidence for the etiology and biomarkers for the prevention and treatment of ESCC.

Tumor Cell Derived Exosomal GOT1 Suppresses Tumor Cell Ferroptosis to Accelerate Pancreatic Cancer Progression by Activating Nrf2/HO-1 Axis via Upregulating CCR2 Expression

Recently, evidence has shown that GOT1 expression is upregulated in pancreatic cancer tissues and promotes cancer development, but the specific mechanism remains unclear. We found that GOT1 expression was upregulated in pancreatic cancer cell-derived exosomes. When PANC-1 cells were incubated with exosomes alone or transfected together with si-GOT1, we found that exosomes enhanced cell proliferation, invasion and migration, promoted ferroptosis, and si-GOT1 reversed the effects of exosomes. The results of online bioinformatics database analysis indicated that CCR2 was a potential binding protein of GOT1 and is highly expressed in pancreatic cancer tissues. PANC-1 cells were transfected with pcDNA-CCR2 or si-CCR2, and it was found that pcDNA-CCR2 enhanced cell proliferation, invasion and migration, promoted ferroptosis, and si-CCR2 had an opposite effect. Next, exosome-treated cells were transfected with si-GOT1 alone or together with pcDNA-CCR2, and we found that exosomes promoted CCR2 expression, promoted cell proliferation and invasion, and inhibited ferroptosis, the transfection of si-GOT1 abolished the effect of exosomes, and the transfection of pcDNA-CCR2 again reversed the effect of si-GOT1. Furthermore, when exosome-treated cells were transfected with si-GOT1 alone or co-incubated with Nrf2 activator NK-252, we found that si-GOT1 reversed the promoting effect of exosomes on Nrf2 and HO-1 expression, as well as its inhibitory effect on ferroptosis, but this effect was abrogated by NK-252. In vivo studies showed that knockdown of GOT1 expression inhibited tumor formation compared with tumor tissues formed upon exosome induction, which was mediated by promoting ferroptosis via suppressing the protein expression of GOT1, CCR2, Nrf2 and HO-1 in tumor tissues.

LncRNA-ZNF252P-AS1/miR-15b-5p promotes the proliferation of keloid fibroblast by regulating the BTF3-STAT3 signaling pathway

BackgroundJAK2/STAT3 signaling pathway plays an important role in keloid formation, but the upstream mechanism of their activation remains unclear. ObjectiveThis study aims to investigate the possible mechanism of lncRNA-ZNF252P-AS1 in keloid. MethodsThe differentially expressed genes in keloid and their upstream regulatory miRNAs and long non-coding RNAs (lncRNAs) were analyzed by bioinformatics database, and the targeting relationship was further verified by dual-luciferase reporter gene assay. LncRNA function as competitive endogenous RNA (ceRNA) in keloid was further verified by in keloid fibroblasts (KFs) and in nude mice with subcutaneous keloids. ResultsBTF3 expression was up-regulated in keloid tissues. The targeting relationship between BTF3 and miR-15b-5p was confirmed by dual-luciferase reporter gene assay. miR-15b-5p overexpression inhibited BTF3, Bcl-2, Cyclin D1, C-myc, Collagen I, MMP2, MMP9, N-cadherin, and ZEB2 expressions in KFs, inhibited cell proliferation and migration, while promoted E-cadherin levels. BTF3 overexpression reversed miR-15b-5p effects on KFs. Bioinformatics analysis as well as clinical and cellular experiments confirmed that the lncRNA ZNF252P-AS1 was highly expressed in keloid/KFs. Dual-luciferase reporter gene assays confirmed the targeting relationship between lncRNA ZNF252P-AS1 and miR-15b-5p. LncRNA ZNF252P-AS1 overexpression inhibited miR-15b-5p and E-cadherin levels, upregulated BTF3, Bcl-2, Cyclin D1, C-myc, Collagen I, MMP2, MMP9, N-cadherin, and ZEB2 expressions, increased cell proliferation and migration, and activated JAK2/STAT3 pathway, while miR-15b-5p overexpression reversed this effect. The in vivo results were consistent with in vitro results. In vivo experiments further confirmed that lncRNA ZNF252P-AS1 reduced keloid volume and weight. ConclusionlncRNA ZNF252P-AS1 is a potential target for keloid treatment.

Structural Analysis and Diversity of Calmodulin-Binding Domains in Membrane and Intracellular Ca2+-ATPases.

The plasma membrane and autoinhibited Ca2+-ATPases contribute to the Ca2+ homeostasis in a wide variety of organisms. The enzymatic activity of these pumps is stimulated by calmodulin, which interacts with the target protein through the calmodulin-binding domain (CaMBD). Most information about this region is related to all calmodulin modulated proteins, which indicates general chemical properties and there is no established relation between Ca2+ pump sequences and taxonomic classification. Thus, the aim of this study was to perform an in silico analysis of the CaMBD from several Ca2+-ATPases, in order to determine their diversity and to detect specific patterns and amino acid selection in different species. Patterns related to potential and confirmed CaMBD were detected using sequences retrieved from the literature. The occurrence of these patterns was determined across 120 sequences from 17 taxonomical classes, which were analyzed by a phylogenetic tree to establish phylogenetic groups. Predicted physicochemical characteristics including hydropathy and net charge were calculated for each group of sequences. 22 Ca2+-ATPases sequences from animals, unicellular eukaryotes, and plants were retrieved from bioinformatic databases. These sequences allow us to establish the Patterns 1(GQILWVRGLTRLQTQ), 3(KNPSLEALQRW), and 4(SRWRRLQAEHVKK), which are present at the beginning of putative CaMBD of metazoan, parasites, and land plants. A pattern 2 (IRVVNAFR) was consistently found at the end of most analyzed sequences. The amino acid preference in the CaMBDs changed depending on the phylogenetic groups, with predominance of several aliphatic and charged residues, to confer amphiphilic properties. The results here displayed show a conserved mechanism to contribute to the Ca2+ homeostasis across evolution and may help to detect putative CaMBDs.

Mass spectrometry in snake venom research

Mass spectrometry allows rapid and reliable identification and characterisation of proteins and peptides in snake venoms. With the increasing availability of transcriptomic and genomic data, there is a growing database of protein sequences that is essential for protein identification. Snake venoms are analysed using a multi-dimensional proteomic approach known as ‚venomics‘. Proteins are first separated by one- or two-dimensional gel electrophoresis or reversed-phase liquid chromatography. The individual protein spots or fractions are digested enzymatically and the resulting peptides are analysed by mass spectrometry. The proteins are identified by comparing the mass spectra of the peptides with those in the database. High-performance mass spectrometers allow the analysis of venoms even without prior separation of the protein mixture. We have analysed the protein composition (proteome) of two European snake venoms of greatest medical interest, the nose-horned viper (Vipera a. ammodytes) and the common adder (Vipera b. berus). The nose-horned viper is the most venomous European snake. Although its bite is rarely fatal, a human wictim often needs to be observed in hospital and treated with an antivenom. The adder is the most widespread European venomous snake and its bite causes milder symptoms than the bite of the nose-horned viper in most cases. To explain the observed differences in the effects of the two venoms at the molecular level, a proteomic study was performed. We also analysed the proteome of the venom of the meadow viper (Vipera ursinii), the most threatened snake species in Europe. It does not pose a threat to humans. In the wild, it feeds mainly on insects, while in captivity it is fed on mice. A comparison of the proteome of the venom of snakes in the wild and snakes in captivity showed clear differences. Thus, the composition of snake venom is diet-dependent. Mass spectrometry is also a very useful tool in the characterisation of antivenoms (antivenomics) to determine their specificity and neutralising power.

Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir.

As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.

Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait

BackgroundAverage backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS. ResultsIn this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified.ConclusionQTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.

In silico and in vitro analysis of microRNAs with therapeutic potential in atherosclerosis

Atherosclerosis is a chronic inflammatory disease in which aberrant lipid metabolism plays a key role. MicroRNAs (miRNAs), micro-coordinators of gene expression, have been recently proposed as novel clinical biomarkers and potential therapeutic tools for a broad spectrum of diseases. This study aimed to identify miRNAs with therapeutic potential in atherosclerosis. Bioinformatic databases, including experimentally validated and computational prediction tools as well as a novel combination method, were used to identify miRNAs that are able to simultaneously inhibit key genes related to the pathogenesis of atherosclerosis. Further validation of genes and miRNAs was conducted using the STRING online tool, KEGG pathway analysis and DIANA-miRPath. The inhibitory effects of the identified miRNAs in HepG2 and Huh7 cells were verified by real-time PCR. The MTT assay was utilized to evaluate cell cytotoxicity effects of miRNAs. Atherosclerotic drug-targeted genes were selected as key genes. Strong interactions between genes were confirmed using STRING. These genes were shown to be integral to critical pathological processes involved in atherosclerosis. A novel combined method of validated and predicted tools for the identification of effective miRNAs was defined as the combination score (C-Score). Bioinformatic analysis showed that hsa-miR-124-3p and hsa-miR-16-5p possessed the best C-Score (0.68 and 0.62, respectively). KEGG and DIANA-miRPath analysis showed that selected genes and identified miRNAs were involved in atherosclerosis-related pathways. Compared with the controls in both HepG2 and Huh7 cell lines, miR-124 significantly reduced the expression of CETP, PCSK9, MTTP, and APOB, and miR-16 significantly reduced the expression of APOCIII, CETP, HMGCR, PCSK9, MTTP, and APOB, respectively. The cytotoxicity assay showed that miR-124 reduced cell viability, especially after 72 h; however, miR-16 did not show any significant cytotoxicity in either cell line. Our findings indicate that hsa-miR-124 and miR-16 have potential for use as therapeutic candidates in the treatment of atherosclerosis.

Prognostic value and immune infiltration of the gasdermin family in lung adenocarcinoma.

The GSDM family includes six members, GSDMA, GSDMB, GSDMC, GSDMD, GSDME (DFNA5), and PJVK (Pejvakin, DFNB59), which can induce pyroptosis, thereby regulating the tumorigenesis of various cancers. However, the clinical characteristics and role of the GSDM family in LUAD are not well understood. In this study, several important bioinformatics databases were used to integrate the analysis of the expression, prognostic value, and immune infiltration of GSDMs in LUAD. These databases include UALCAN, DiseaseMeth, GEPIA, THPA, cBioPortal, TIMER, WebGestalt, STRING database, and Cytoscape. The findings from the UALCAN database revealed that the expression of all six GSDMs based on the tumor stage in LUAD was increased (particularly GSDMD). Our IHC results verified it. Additionally, the DiseaseMeth database showed that the methylation levels of GSDMA, GSDMB, GSDMC, and GSDMD were decreased. The expression of six GSDMs was related to shorter overall survival in patients with LUAD, according to the GEPIA database. The cBioPortal database was further used to explore the alteration rate and correlated genes in LUAD. Subsequently, these genes were subjected to functional enrichment and protein-protein interaction network analyses. We identified that the GSDM family regulate several signaling pathways, including immune-associated signaling pathways. According to tumor-infiltrating immune cell analysis from the TIMER database, GSDM family members are associated with the infiltration of important immune cells and their signature markers. GSDM family may be prognostic markers and novel strategies for the treatment of LUAD.

Molecular Mechanisms Underlying the Effect of Paeoniae Radix Rubra on Sepsis-Induced Coagulopathy: A Network Pharmacology and Molecular Docking Approach

Abstract To investigate the effective components and underlying mechanism of Paeoniae radix rubra (PRR) in treating sepsis-induced coagulopathy (SIC) on the basis of network pharmacology and molecular docking approaches. At present, no therapeutic agent has been approved for the treatment of SIC. Identifying drugs for SIC from Chinese medicine is an encouraging research direction. The predicted targets and effective components of PRR were identified by analysis of the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. Bio-informatics databases were employed to identify the disease targets of SIC. These key targets were then uploaded to the STRING database to generate protein–protein interaction networks. The ORG package in rv4.1.2 software was applied for functional and pathway enrichment analyses of the key targets. Finally, discovery studio software was used to perform docking analyses of key targets and effective components. Nine chemically active components and 84 common targets associated with drugs and SIC were identified. Protein–protein interaction (PPI) network analysis identified several key targets. Further analysis identified enrichment in several signaling pathways; these changes could exert influence on a number of biological processes, including responses to xenobiotic stimuli, oxidative stress, molecules of bacterial origin, thus playing an anti-SIC pharmacological role. According to molecular docking results, these key targets had strong binding affinity to the active components. PRR can contribute to SIC by medicating core target genes (e.g., CASP3, PTGS2, TP53, AKT1, MMP9, TNF, JUN, IL6, and CXCL8), and regulating multiple key pathways (e.g., the lipid and atherosclerosis pathway).

JUND/linc00976 promotes cholangiocarcinoma progression and metastasis, inhibits ferroptosis by regulating the miR-3202/GPX4 axis

Long noncoding RNAs (lncRNAs) are a novel class of noncoding RNAs that have emerged as critical regulators and biomarkers in various cancers. Nevertheless, the expression profile and mechanistic function of lncRNAs in cholangiocarcinoma (CCA) remain unclear. Herein, we examined the expression levels of linc00976 in clinical specimens and cell lines using reverse transcription-quantitative PCR. In total, 50 patients with CCA were enrolled to analyze the correlation between linc00976 expression and clinical characteristics of CCA. Loss- and gain-of-function experiments were performed to investigate the biological effects of linc00976 on proliferation, ferroptosis, migration, and invasion of CCA cells in vitro and in vivo. In situ hybridization, RNA immunoprecipitation, bioinformatic databases, RNA pull-down assay, a dual-luciferase reporter assay, mRNA sequencing, chromatin immunoprecipitation–PCR, and rescue experiments were performed to elucidate the underlying mechanisms of linc00976-induced competitive endogenous RNA regulatory networks. We characterized a novel and abundant lncRNA, linc00976, that functions as a pro-oncogenic regulator of CCA progression. Compared with normal controls, linc00976 was dramatically upregulated in CCA tissue samples and cell lines. Patients with CCA exhibiting high linc00976 expression had a highly advanced clinical stage, substantial lymph node metastasis, and poor overall survival. Knockdown of linc00976 significantly repressed proliferation and metastasis and promoted ferroptosis of CCA cells both in vitro and in vivo, whereas linc00976 overexpression exerted the opposite effect. Mechanistically, linc00976 competitively interacted with miR-3202 to upregulate GPX4 expression, thus contributing to the malignant biological behavior of CCA cells. Moreover, we demonstrated that JUND specifically interacts with the linc00976 promoter and activates linc00976 transcription. Accordingly, JUND promotes linc00976 transcription, and linc00976 plays a crucial role in accelerating CCA tumorigenesis and metastasis and inhibiting ferroptosis by modulating the miR-3202/GPX4 axis. These findings suggest that targeting linc00976 may afford a promising therapeutic strategy for patients with CCA.

Bioinformatics in Plant Breeding and Research on Disease Resistance.

In the context of plant breeding, bioinformatics can empower genetic and genomic selection to determine the optimal combination of genotypes that will produce a desired phenotype and help expedite the isolation of these new varieties. Bioinformatics is also instrumental in collecting and processing plant phenotypes, which facilitates plant breeding. Robots that use automated and digital technologies to collect and analyze different types of information to monitor the environment in which plants grow, analyze the environmental stresses they face, and promptly optimize suboptimal and adverse growth conditions accordingly, have helped plant research and saved human resources. In this paper, we describe the use of various bioinformatics databases and algorithms and explore their potential applications in plant breeding and for research on plant disease resistance.

EP300-ZNF384 Rearrangement Drive B-Cell Acute Lymphoblastic Leukemia Development By Activating IL3-IL3RA Signaling

Abstract: EP300-ZNF384 chromosome rearrangement serves as an oncogenic driver in B-cell acute lymphoblastic leukemia development. However, the oncogenic mechanisms underlying EP300-ZNF384 remain largely elusive. Recent evidence shows that the gene expression signature in EP300-ZNF384-positive patients enriched in cytokine-cytokine receptor and JAK-STAT signaling. We reason the correlated cytokine-cytokine receptor and JAK-STAT signaling might play important roles in EP300-ZNF384 fusion primed B-cell acute lymphoblastic leukemia. To investigate this concept, we identified EP300-ZNF384 substantially induces the expression of IL3RA on cell membranes of B lineage cells. Further, we proved IL3 supplement promotes EP300-ZNF348 positive cells proliferation and colony formation by activating JAK-STAT signaling. IL3RA knockdown reduces the responsiveness of EP300-ZF384 positive cells to IL3 stimulation. Dual luciferase assay and ChIP-qPCR assay confirm that EP300-ZNF384 binds the promoter region of IL3RA and actives its transcription. Interestingly, IL3 expression was significantly upregulated in ZNF384 rearranged B-cell acute lymphoblastic leukemia patients comparing with B others through analyzing bioinformatics databases. These findings underscore the critical role of IL3-IL3RA signaling under EP300-ZNF384 driven B-cell acute lymphoblastic leukemia and imply EP300-ZNF384 positive patients might benefit from JAK inhibitors. Keywords: EP300-ZNF384, B-cell Acute Lymphoblastic leukemia, IL3RA, IL3 JAK, STAT

Bioinformatics analysis and function prediction of NBS-LRR gene family in Broussonetia papyrifera.

Most of the currently available disease resistance (R) genes have NBS (nucleotide-binding site) and LRR (leucine-rich-repeat) domain which belongs to the NBS-LRR gene family. The whole genome sequencing of Broussonetia papyrifera provides an important bioinformatics database for the study of the NBS-LRR gene family. In this study, 328 NBS-LRR family genes were identified and classified in B. papyrifera according to different classification schemes, where there are 92N types, 47 CN type, 54 CNL type, 29 NL types, 55 TN type, and 51 TNL type. Subsequently, we conducted bioinformatics analysis of the NBS-LRR gene family. Classification, motif analysis of protein sequences, and phylogenetic tree studies of the NBS-LRR genes in B. papyrifera provide important basis for the functional study of NBS-LRR family genes. Additionally, we performed structural analysis of the chromosomal location, physicochemical properties, and sequences identified by genetic characterization. In addition, through the analysis of GO enrichment, it was found that NBS-LRR genes were involved in defense responses and were significantly enriched in biological stimulation, immune response, and abiotic stress. In addition, we found that Bp06g0955 was the most sensitive to low temperature and encoded the RPM1 protein by analyzing the low temperature transcriptome data of B. papyrifera. Quantitative results of gene expression after 48h of Fusarium infection showed that Bp01g3293 increased 14 times after infection, which encodes RPM1 protein. The potential of NBS-LRR gene responsive to biotic and abiotic stresses can be exploited to improve the resistance of B. papyrifera.

Comprehensive analysis of plasma miRNA and related ceRNA network in non-syndromic cleft lip and/or palate.

Non-syndromic cleft lip and/or palate (NSCL/P) is a common maxillofacial birth defect, and the etiology of which is complex and still unclear. Accumulating studies indicate that long non-coding RNAs(lncRNAs) and microRNAs(miRNAs) play important roles in NSCL/P. However, the potential regulatory associations remain largely unknown. In this study, we screened differentially expressed miRNAs and constructed competing endogenous RNA (ceRNA) networks to lay a foundation for further research on the regulatory mechanism of ncRNAs in NSCL/P. NSCL/P plasma RNA was analyzed by miRNA sequencing. The bioinformatics database, GEO and STRING database, GO and KEGG enrichment analysis and Cytoscape software were used to analyze and screen lncRNAs and mRNAs potentially related to differential miRNAs. The expression levels of lncRNA, miRNA and mRNA in ceRNA network were detected by RT-qPCR. In NSCL/P plasma samples, there were 47 differentially expressed miRNAs in CPO group and 36 differentially expressed miRNAs in CL/P group. GO and KEGG enrichment analysis showed that cell cycle, cell response to DNA damage stimulation, and the TGF-βsignaling pathway were relevant to the formation of NSCL/P. The RT-qPCR results showed that the expression levels of lncRNA NEAT1, hsa-miR-130b-3p, hsa-miR-212-3p, hsa-miR-200b-3p and SMAD2 were different in NSCL/P. We found that differentially expressed miR-212-3p, miR-200b-3p and miR-130b-3p may be involved in the pathogenesis of cleft palate by regulating related target genes.